Programming knowledge is often necessary for finding a solution to a biological problem. Based on the author’s experience working for an agricultural biotechnology company, Python for Bioinformatics helps scientists solve their biological problems by helping them understand the basics of programming. Requiring no prior knowledge of programming-related concepts, the book focuses on the easy-to-use, yet powerful, Python computer language.
The book begins with a very basic introduction that teaches the principles of programming. It then introduces the Biopython package, which can be useful in solving life science problems. The next section covers sophisticated tools for bioinformatics, including relational database management systems and XML. The last part illustrates applications with source code, such as sequence manipulation, filtering vector contamination, calculating DNA melting temperature, parsing a genbank file, inferring splicing sites, and more. The appendices provide a wealth of supplementary information, including instructions for installing Python and Biopython and a Python language and style guide.
By incorporating examples in biology as well as code fragments throughout, the author places a special emphasis on practice, encouraging readers to experiment with the code. He shows how to use Python and the Biopython package for building web applications, genomic annotation, data manipulation, and countless other applications.
First Steps with Python
Basic Programming: Data Types
Programming: Flow Control
Dealing with Files
Introduction to Object Orienting Programming (OOP)
Introduction to Biopython
Python and Databases
Collaborative Development: Version Control
PYTHON RECIPES WITH COMMENTED SOURCE CODE
Sequence Manipulation in Batch
Web Application for Filtering Vector Contamination
Searching for PCR Primers Using Primer3
Calculating Melting Temperature from a Set of Primers
Filtering out Specific Fields from a Genbank File
Converting XML Blast File into HTML
Inferring Splicing Sites
DNA Mutations with Restrictions
Web Server for Multiple Alignment
Drawing Marker Positions Using Data Stored in a Database
Appendix A: Python and Biopython Installation
Appendix B: Selected Papers
Appendix C: Included DVD: Virtual Machine Installation and Use
Appendix D: Python Language Reference
Appendix E: Answers to Odd-Numbered Questions
Appendix F: Python Style Guide
Sebastian Bassi is the leader of the DNALinux bioinformatics distribution and member of the developer team for Biopython. He is currently providing bioinformatics support for the tomato mitochondrial genome sequencing project, which is part of the Latin America Solanaceae Genome Project (LAT-SOL).
The book will be helpful for its intended audience. Numerous code fragments in the book will be beneficial for biologists who are unfamiliar with programming. Readers can try out, test, and modify the code to suit their needs. … a useful introduction to the topic. The style of presentation is good, and the code samples are worthwhile. … I strongly recommend this book as a useful reference for computational biologists, programmers, and bioinformatics specialists (students as well as researchers).
—Computing Reviews, November 2011